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We report measurements by Chandra of a variety of X-ray sources in the molecular clouds and HII regions of the Sgr B2, Arches, Quintuplet and the Galactic center clusters. Moderately bright X-ray sources are present in the Sgr B2, Quintuplet and the Galactic center clusters at the positions of ultra compact HII regions and bright infrared sources. Their X-ray spectra are fitted with models of a thin thermal plasma with 2–10 keV temperatures and luminosities of ∼1032–33erg s−1. The X-ray properties are typical of those of high-mass young stellar objects or clusters of such objects. The Arches Cluster has three bright X-ray sources, at the positions of bright IR and radio stars, with X-ray luminosities of a few ×1033 erg s−1 each, which may indicate an unusual X-ray emission mechanism from high mass YSOs. A unique X-ray feature of molecular clouds and HII regions near the Galactic center is the presence of diffuse emission with a strong 6.4 keV line; in Sgr B2 this is attributable to the fluorescence of gas irradiated by external sources in the Galactic center, while the diffuse emission from Arches is puzzling.